The general long-term objectives of this project are to develop theories and statistical methods tp analyze the genetic architecture of quantitative traits (including mapping of quantitative trait loci) and to learn the genetic and evolutionary bases of quantitative trait variation within and between natural and experimental populations. The specific goal of the current application is to develop and extend theory and statistical methods to map quantitative trait loci (QTL) and to estimate the whole genetic architecture (GA) of quantitative traits in inbred cross populations, in large full-sib families, and in natural random mating populations. The methods are generally based on the multiple interval mapping (MIM) approach we developed for inbred cross populations. For natural populations, new methods will be developed. Specifically, we propose to: Standardize, evaluate and implement MIM for mapping QTL and estimating GA of quantitative traits in a variety of cross populations from inbred lines. Develop systematic methods for mapping QTL and estimating GA parameters in full-sib families with massive dominant markers. Explore the possibility to use single nucleotide polymorphism (SNP) markers to directly infer GA of a quantitative trait in a natural random mating populations and also study associated statistical methods and issues.